I believe this is still a bug. I experienced it with Adobe Premiere Pro CC 2018 today.
I have a mulitcam sequence (2 cameras) with several tight audio edits. While listening to the sequence, things sounded fine. After exporting via the Queue in Adobe Media Encoder, there were blips and other noises (sounding like they came from the unused audio track from camera 2).
Thanks to others on this thread, I was able to work around it by exporting the sequence directly out of Premiere.
( File/Export. Then, when the AME interface pops up, select Export, rather than Queue.)
Thanks to those posting the workaround as you saved me a lot of time and angst. And you made me a member of Creative Cow!
BTW, I am using:
Adobe Premiere Pro V 12.0.0 (Build 224)
OSX El Capitan 10.11.6 (15G17023)
Mac Pro (Late 2013)
3.5 GHz 6-Core Intel Xeon E5
64 Gig Memory
AMD FirePro D500 3072 MB Graphics Card